def mod_udf(self, uin, pre, direction, lamd):
time_1_step = round(self.resol/self.time_div/self.rate, -2)
time_total = round(time_1_step*(lamd - 1)/self.resol, -2)
#
udf = UDFManager(uin)
udf.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
udf.put(time_total, p + 'Time.Total_Steps')
udf.put(time_1_step, p + 'Time.Output_Interval_Steps')
if direction == 'backward':
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
srate = udf.get(p + 'Cell_Deformation.Simple_Elongation.Deformation_Speed.Speed')
udf.put(-1*srate, p + 'Cell_Deformation.Simple_Elongation.Deformation_Speed.Speed')
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
udf.put('Restart', p + 'Method')
udf.put([pre, -1, 1, 0], p + 'Restart')
#--- Write UDF ---
udf.write(uin)
return
def mod_udf(self, udf_in, rate):
if self.def_mode == 'elong':
time_1_step = int(self.res/self.time_div/rate)
time_total = time_1_step*(self.deform_max - 1)/self.res
elif self.def_mode == 'shear':
deform_time = self.deform_max/rate
time_total = round(deform_time/self.time_div)
time_1_step = int(self.res/self.time_div/rate)
#
u = UDFManager(udf_in)
# goto global data
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(self.time_div, p + 'Time.delta_T')
u.put(time_total, p + 'Time.Total_Steps')
u.put(time_1_step, p + 'Time.Output_Interval_Steps')
u.put(1.0, p + 'Temperature.Temperature')
u.put(0, p + 'Temperature.Interval_of_Scale_Temp')
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
if self.def_mode == 'elong':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate', p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(rate, p + 'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
elif self.def_mode == 'shear':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Lees_Edwards', p + 'Method')
u.put('Steady', p + 'Lees_Edwards.Method')
u.put(rate, p + 'Lees_Edwards.Steady.Shear_Rate')
# Output_Flags
u.put([1, 1, 1], 'Simulation_Conditions.Output_Flags.Structure')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put(['', -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put(['', -1, 1, 1], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
#--- Write UDF ---
u.write(udf_in)
return
def eq_udf(self, template, read_udf, present_udf, time_temp):
u = UDFManager(os.path.join(self.calc_dir, template))
u.jump(-1)
#--- Simulation_Conditions ---
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(time_temp[0], p+'Time.delta_T')
u.put(time_temp[1], p+'Time.Total_Steps')
u.put(time_temp[2], p+'Time.Output_Interval_Steps')
u.put(time_temp[4], p + 'Temperature.Interval_of_Scale_Temp')
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('None', p + 'Method')
#--- Initial_Structure ---
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put([self.base_udf, -1], p)
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p+'Method')
u.put([read_udf, -1, 1, 1], p+'Restart')
#--- Write UDF ---
u.write(os.path.join(self.calc_dir, present_udf))
return
def step_elong(self, base, udf_in, time_temp):
u = UDFManager(base)
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(time_temp[0], p + 'Time.delta_T')
u.put(time_temp[1], p + 'Time.Total_Steps')
u.put(time_temp[2], p + 'Time.Output_Interval_Steps')
#
u.put(1.0, p + 'Temperature.Temperature')
u.put(time_temp[4], p + 'Temperature.Interval_of_Scale_Temp')
#
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate', p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(self.step_rate, p + 'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put([self.base_udf, -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put([self.base_udf, -1, 1, 1], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
#--- Write UDF ---
u.write(os.path.join(self.calc_dir, udf_in))
return
def mod_udf(self, udf_in, rate):
time_1_step = int(self.res/self.time_div/rate)
time_total = time_1_step*(self.Lamd_max - 1)/self.res
#
u = UDFManager(udf_in)
# goto global data
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(self.time_div, p + 'Time.delta_T')
u.put(time_total, p + 'Time.Total_Steps')
u.put(time_1_step, p + 'Time.Output_Interval_Steps')
u.put(1.0, p + 'Temperature.Temperature')
u.put(0, p + 'Temperature.Interval_of_Scale_Temp')
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate', p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(rate, p + 'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put([self.base_udf, -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put([self.base_udf, -1, 1, 0], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
#--- Write UDF ---
u.write(udf_in)
return
def step_deform(self, base, axis, udf_in, time_temp, target_dir):
u = UDFManager(base)
u.jump(-1)
# Dynamics_Conditions
p = 'Simulation_Conditions.Dynamics_Conditions.'
u.put(100000., p + 'Max_Force')
u.put(time_temp[0], p + 'Time.delta_T')
u.put(time_temp[1], p + 'Time.Total_Steps')
u.put(time_temp[2], p + 'Time.Output_Interval_Steps')
#
u.put(1.0, p + 'Temperature.Temperature')
u.put(time_temp[4], p + 'Temperature.Interval_of_Scale_Temp')
#
u.put(0, p + 'Pressure_Stress.Pressure')
# Deformation
if self.mode == 'elong':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Cell_Deformation', p + 'Method')
u.put('Simple_Elongation', p + 'Cell_Deformation.Method')
u.put('Initial_Strain_Rate',
p + 'Cell_Deformation.Simple_Elongation.Input_Method')
u.put(
self.step_rate, p +
'Cell_Deformation.Simple_Elongation.Initial_Strain_Rate.Rate')
u.put(0.5, p + 'Cell_Deformation.Simple_Elongation.Poisson_Ratio')
u.put('z', p + 'Cell_Deformation.Simple_Elongation.Axis')
u.put(1, p + 'Cell_Deformation.Interval_of_Deform')
u.put(0, p + 'Cell_Deformation.Deform_Atom')
elif self.mode == 'shear':
p = "Simulation_Conditions.Dynamics_Conditions.Deformation."
u.put('Lees_Edwards', p + 'Method')
u.put('Steady', p + 'Lees_Edwards.Method')
u.put(self.step_rate, p + 'Lees_Edwards.Steady.Shear_Rate')
# Output_Flags
u.put([1, 1, 1], 'Simulation_Conditions.Output_Flags.Structure')
# Read_Set_of_Molecules
p = 'Initial_Structure.Read_Set_of_Molecules'
u.put(['', -1], p)
# Generate_Method
p = 'Initial_Structure.Generate_Method.'
u.put('Restart', p + 'Method')
u.put(['', -1, 1, 1], p + 'Restart')
# Relaxation
p = 'Initial_Structure.Relaxation.'
u.put(0, p + 'Relaxation')
# Rotate system
self.rotate_position(u, axis)
#--- Write UDF ---
u.write(os.path.join(target_dir, udf_in))
return